Samples before QC filtering

Zero samples are removed based on sample-QC metrics

QC Summary Table for each Segment
Pass Warning
LowReads 83 0
LowTrimmed 83 0
LowStitched 83 0
LowAligned 83 0
LowSaturation 83 0
LowNegatives 83 0
HighNTC 83 0
LowArea 83 0
TOTAL FLAGS 83 0

Based on per-probe quality control, Only one probe is removed

##   Passed Global Local
## 1  18813      1     1

DESeq with total data

Plot PCA for transformed count data

Dimension Reduction on normalized counts (UMAP)

## Heatmap of correlation between samples

Subset endocrine samples

PCA of normalized counts (endocrine)

Dimension Reduction (endocrine)

## Heatmap of correlation between samples (endocrine) ### Suggests body roi share expression profile

Because the body roi are distinct, we do DE analysis with body as the control

Differential Expression Results

Visualize expression of DE genes in three pancreas regions relative to expression in the body of the pancreas

## Warning: Duplicated aesthetics after name standardisation: size
## Duplicated aesthetics after name standardisation: size

## Warning: Duplicated aesthetics after name standardisation: size

### Look at the expression of genes identified as DE in the head region relative to other regions

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## Subset exocrine samples

PCA of normalized counts (exocrine)

Dimension Reduction (exocrine)

## Heatmap of correlation between samples (exocrine) ### Suggests body roi share expression profile

No group of roi are distinct based on region, but we can do DE analysis with body as the control

Just to see how it compares to endocrine results

Visualize expression of DE genes in three pancreas regions relative to expression in the body of the pancreas

## Warning: Duplicated aesthetics after name standardisation: size
## Duplicated aesthetics after name standardisation: size

## Warning: Duplicated aesthetics after name standardisation: size

### Look at the expression of genes identified as DE in the head region relative to any other region

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